Tuesday, April 01, 2008

The Nitrogen Cycle

From Horton et al. (2006).

The nitrogen needed for amino acids (and for the heterocyclic bases of nucleotides) comes from two major sources: nitrogen gas in the atmosphere and nitrate (NO3⊖) in soil and water. Atmospheric N2 which constitutes about 80% of the atmosphere, is the ultimate source of biological nitrogen. This molecule can be metabolized, or fixed, by only a few species of bacteria. N2 and NO3⊖ must be reduced to ammonia in order to be used in metabolism. The ammonia produced is incorporated into amino acids via glutamate, glutamine, and carbamoyl phosphate.

N2 is chemically unreactive because of the great strength of the triple bond (N≡N). Some bacteria have a very specific, sophisticated enzyme—nitrogenase1—that can catalyze the reduction of N2 to ammonia in a process called nitrogen fixation. In addition to biological nitrogen fixation there are two additional nitrogen-converting processes. During lightning storms, high-voltage discharges cause the oxidation of N2 to nitrate and nitrite (NO2⊖). Industrially, nitrogen is converted to ammonia for use in plant fertilizers by an energetically expensive process that requires high temperature and pressure as well as special catalysts to drive the reduction of N2 by H2. The availability of biologically useful nitrogen is often a limiting factor for plant growth, and the application of nitrogenous fertilizers is important for obtaining high crop yields. Although only a small percentage of the nitrogen undergoing metabolism comes directly from nitrogen fixation, this process is the only way that organisms can use the huge pool of atmospheric N2.

The overall scheme for the interconversion of the major nitrogen-containing compounds is shown in Figure 17.1. The flow of nitrogen from N2 to nitrogen oxides, ammonia, and nitrogenous biomolecules and then back to N2 is called the nitrogen cycle. Most of the nitrogen shuttles between ammonia and nitrate. Ammonia from decayed organisms is oxidized by soil bacteria to nitrate. This formation of nitrate is called nitrification. Some anaerobic bacteria can reduce nitrate or nitrite to N2 (denitrification). Most green plants and some microorganisms contain nitrate reductase and nitrite reductase, enzymes that together catalyze the reduction of nitrogen oxides to ammonia.This ammonia is used by plants, which supply amino acids to animals. Reduced ferredoxin (formed in the light reactions of photosynthesis) is the source of the reducing power in plants and photosynthetic bacteria.

Let’s examine the enzymatic reduction of N2. Most nitrogen fixation in the biosphere is carried out by bacteria that synthesize the enzyme nitrogenase. This multisubunit protein catalyzes the conversion of each molecule of N2 to two molecules of NH3 (ammonia). Nitrogenase is present in various species of Rhizobium and Bradyrhizobium that live symbiotically in root nodules of many leguminous plants, including soybeans, peas, alfalfa, and clover (Figure 17.2). N2 is also fixed by freeliving soil bacteria such as Agrobacteria, Azotobacter, Klebsiella, and Clostridium and by cyanobacteria (mostly Trichodesmium spp.) found in the ocean. Most plants require a supply of fixed nitrogen from sources such as decayed animal and plant tissue, nitrogen compounds excreted by bacteria, and fertilizers. Vertebrates obtain fixed nitrogen by ingesting plant and animal matter.

Nitrogenase is a protein complex that consists of two different polypeptide subunits with a relatively complicated electron-transport system. One polypeptide (called iron protein) contains a [4 Fe–4 S] cluster, and the other (called iron–molybdenum protein) has two oxidation–reduction centers, one containing iron in an [8 Fe–7 S] cluster, and the other containing both iron and molybdenum. Nitrogenases must be protected from oxygen because the metalloproteins are highly susceptible to inactivation by O2. For example, strict anaerobes carry out nitrogen fixation only in the absence of O2. Within the root nodules of leguminous plants, the protein leghemoglobin (a homolog of vertebrate myoglobin) binds and thereby keeps its concentration sufficiently low in the immediate environment of the nitrogen-fixing enzymes of rhizobia. Nitrogen fixation in cyanobacteria is carried out in specialized cells (heterocysts) whose thick membranes inhibit entry of O2.

A strong reducing agent—either reduced ferredoxin or reduced flavodoxin (a flavoprotein electron carrier in microorganisms)—is required for the enzymatic reduction of N2 to NH3. An obligatory reduction of 2 H⊕ to H2 accompanies the reduction of N2. For each electron transferred by nitrogenase, at least two ATP molecules must be converted to ADP and Pi (inorganic phosphate) so the six-electron reduction of a single molecule of N2 (plus the two-electron reduction of 2 H⊕) consumes a minimum of 16 ATP.

In order to obtain the reducing power and ATP required for this process, symbiotic nitrogen-fixing microorganisms rely on nutrients obtained through photosynthesis carried out by the plants with which they are associated.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.